Merge 7986aff into 1bdf204

lib/Bio/EnsEMBL/DataCheck/Checks/ExonRank.pm

@@ -0,0 +1,55 @@
+=head1 LICENSE
+
+Copyright [2018] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the 'License');
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an 'AS IS' BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::ExonRank;
+
+use warnings;
+use strict;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+use Moose;
+use Test::More;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+    NAME        => 'ExonRank',
+    DESCRIPTION => 'Check for entries in the exon_transcript table that are duplicates apart from the rank',
+    GROUPS      => [ 'core_handover' ],
+    DB_TYPES    => [ 'core' ]
+};
+
+sub tests {
+    my ($self) = @_;
+
+    my $descexon_rank = 'Exon/Transcript rank count';
+    my $diagexon_rank = "Same Exon/Transcript with different ranks";
+    my $sqlexon_rank = qq/
+        SELECT  exon_id,
+                transcript_id,
+                GROUP_CONCAT(`rank` SEPARATOR '-')
+        FROM exon_transcript
+        GROUP BY exon_id, transcript_id
+        HAVING COUNT(`rank`) > 1
+    /;
+    is_rows_zero($self->dba, $sqlexon_rank, $descexon_rank, $diagexon_rank);
+
+}
+
+1;
+

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -195,6 +195,15 @@
       "name" : "EpigenomeHasSegmentationFile",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::EpigenomeHasSegmentationFile"
    },
+   "ExonRank" : {
+      "datacheck_type" : "critical",
+      "description" : "Check for entries in the exon_transcript table that are duplicates apart from the rank",
+      "groups" : [
+         "core_handover"
+      ],
+      "name" : "ExonRank",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::ExonRank"
+   },
    "ExperimentHasFeatureSet" : {
       "datacheck_type" : "critical",
       "description" : "Check that every distinct experiment, epigenome and feature_type combination is linked to a feature_set",